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A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model
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Flexible molecular docking is a computational method of structure-based drug design to evaluate binding interactions between receptor and ligand and identify the ligand conformation within the receptor pocket. Currently, various molecular docking programs are extensively applied; therefore, realizing accuracy and performance of the various docking programs could have a significant value. In this comparative study, the performance and accuracy of three widely used non-commercial docking software (AutoDock Vina, 1-Click Docking, and UCSF DOCK) was evaluated through investigations of the predicted binding affinity and binding conformation of the same set of small molecules (HIV-1 protease inhibitors) and a protein target HIV-1 protease enzyme. The tested sets are composed of eight receptor-ligand complexes with high resolution crystal structures downloaded from Protein Data Bank website. Molecular dockings were applied between approved HIV-1 protease inhibitors and the HIV-1 protease using AutoDock Vina, 1-Click Docking, and DOCK6. Then, docking poses of the top-ranked solution was realized using UCSF Chimera. Furthermore, Pearson correlation coefficient (r) and coefficient of determination (r2) between the experimental results and the top scored docking results of each program were calculated using Graphpad prism V9.2. After comparing saquinavir top scored binding poses of each docking program with the crystal structure, various conformational changes were observed. Moreover, according to the relative comparison between the top ranked calculated ?Gbinding values against the experimental results, r2 value of AutoDock Vina, 1-Click Docking, and DOCK6 were 0.65, 0.41, and 0.005, respectively. The outcome of this study shows that the top scored binding free energy could not produce the best pose prediction. In addition, AutoDock Vina results have the highest correlation with the experimental results.

 

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Publication Date
Sun Oct 19 2025
Journal Name
Lecture Notes In Networks And Systems
Analyzing the Pragmatics of Argumentation in the Arabic Novel Using Artificial Intelligence: An Applied Study on the Granada Trilogy
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Publication Date
Sun Oct 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
Evaluating the performance of Inspector General Office of the Ministry of health in accordance with normative people and people results for the European excellence model EFQM 2013
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Abstract:

Current research has sought to apply the criteria of potential for altmizalaorbi model EFQM 2013 in assessing the performance of the Inspector General's Office/Ministry of health, so as to keep up with a modern and advanced management methods in the evaluation of performance, as well as to link performance to a citizen's life, and it takes him beyond the accepted service capabilities today, but of budget duties between dealers servicing responsibilities and future planning, financial control, competitiveness, human resources needs and maintaining quality and development, as well as the constant quest for continuous improvement, is the spirit of the principle underpinning the European Foundation Quality managemen

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Publication Date
Tue Aug 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
Evaluating the performance of Inspector General office of the Ministry of health in accordance with normative people and people results for the European excellence model EFQM 2013
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Current research sought to evaluate the performance and results of employees in accordance with normative to people and people result for the European model of excellence EFQM 2013 quality management Foundation in the Inspector General's Office/Ministry of health, so as to pursue a modern and advanced management methods in evaluating performance and the performance of the Office's relationship with a citizen's life, since it takes him beyond the accepted service capabilities today, but it became budget duties between dealers servicing responsibilities and future planning, financial control, competitiveness, human resources needs and maintaining quality and continuous improvement and development as well as The primary role of the

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Publication Date
Sat Dec 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Comparison of the method of partial least squares and the algorithm of singular values decomposion to estimate the parameters of the logistic regression model in the case of the problem of linear multiplicity by using the simulation
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The logistic regression model is an important statistical model showing the relationship between the binary variable and the explanatory variables.                                                        The large number of explanations that are usually used to illustrate the response led to the emergence of the problem of linear multiplicity between the explanatory variables that make estimating the parameters of the model not accurate.    

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Publication Date
Mon Oct 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Scenarios for investment of proposed marshes and requirements for success:a case study in the Marshlands of maysan
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  The research aims to presenting a number of scenarios for the investment of the marshes. The problem of research problem was that there is no in-depth analysis of the marshes  environment. The traditional methods of  the environmental analysis are insufficient. The research community is represented by the decision makers in Maysan Governorate. The research led to proposing of three scenarios with statement  the requirements for the success of each one. The most important conclusions are that the three proposed scenarios for marshes investment depend on the availability of the required volunteers for each scenario. The higher the availability of the requirements, the more optimistic the scenario becomes. If t

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Publication Date
Mon May 01 2017
Journal Name
Desalination And Water Treatment
Cadmium removal from simulated chloride wastewater using a novel flow-by fixed bed electrochemical reactor: Taguchi approach
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Publication Date
Tue Dec 01 2020
Journal Name
Baghdad Science Journal
A Modified Support Vector Machine Classifiers Using Stochastic Gradient Descent with Application to Leukemia Cancer Type Dataset
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Support vector machines (SVMs) are supervised learning models that analyze data for classification or regression. For classification, SVM is widely used by selecting an optimal hyperplane that separates two classes. SVM has very good accuracy and extremally robust comparing with some other classification methods such as logistics linear regression, random forest, k-nearest neighbor and naïve model. However, working with large datasets can cause many problems such as time-consuming and inefficient results. In this paper, the SVM has been modified by using a stochastic Gradient descent process. The modified method, stochastic gradient descent SVM (SGD-SVM), checked by using two simulation datasets. Since the classification of different ca

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Publication Date
Wed Feb 01 2023
Journal Name
Chemical Engineering Research And Design
Nickel removal from simulated wastewater using a novel bio-electrochemical cell with packed bed rotating cylinder cathode
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Publication Date
Sat Jun 30 2012
Journal Name
Al-kindy College Medical Journal
VCAM-1 Expression in Endometerium with Human Cytomegalovirus Infection
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Background: To elucidate the possible role of human cytomegalovirus in pregnancy loss through induction of certain pro-inflammatory adhesion molecules.
Methods: Paraffin embedded sections of curate samples were obtained from 34 women had spontaneous abortion, and 5 women had elective termination of pregnancy (as control), and then subjected for immunohistochemistry analysis to detect human cytomegalovirus (HCMV) early protein and VCAM-1 molecule.
Results: Nine out of 34 women with spontaneous abortion were positive for HCMV early protein, with a
significantly higher expression of VCAM-1 in HCMV positive cases as compared with HCMV negative and the control groups (p = 0.05, 0.001 respectively).
Conclusion: HCMV infection may p

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Publication Date
Thu Feb 07 2019
Journal Name
Journal Of The College Of Education For Women
Nominal Ellipsis in English & Arabic and its Influence on the Translation of the Meanings of Some Selected Qurànic Verses ( A Contrastive study ): هدى فالح حسن & جمانة شكيب محمد
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Nominal ellipsis is a linguistic phenomenon found in English and Arabic .It is
based on leaving out a part of a nominal construction or more for the sake of good
style , compactness and connectedness .This phenomenon is found in the language of
the Glorious Qur’an .The study in hand is concerned with how translators handle
translating Qur’anic verses which contain ellipted nouns , i ,e. , to what extent the
translated Qur’anic verses are close to the original ones , and to what extent their
translations serve understanding the meanings of the glorious verses while at the
same time maintaining their beauty in style. The study aims at shedding light on
nominal ellipsis in English and Arabic .The study undertak

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